Clean data for Abundance - size spectra and beavers

Load packages

library(tidyverse)
library(here)
library(knitr)
library(ggdist)

Load raw data:

We are going to load the raw data collected by Ph.D. student Valentin Moser and master sudents / research assistants.

In the folder data/raw you will find data_arthropods_flying.xlsx

This file contains data collected by flying traps like this one:

Dr. Cornelia Twining deploying the flying arthropods trap into Swiss stream. Photo retriaved from here.

d <- readxl::read_xlsx(path = here("data", "raw","data_arthropods_flying.xlsx"), sheet = 1) |> 
select(-c(sort, remarks)) # remove unnecesary column
glimpse(d)

Rows: 6,681
Columns: 14
$ site        <chr> "Chrie", "Chrie", "Chrie", "Chrie", "Chrie", "Chrie", "Chr…
$ location    <chr> "Control", "Control", "Control", "Control", "Control", "Co…
$ date        <chr> "June", "June", "June", "June", "June", "June", "June", "J…
$ class       <chr> "Arachnida", "Arachnida", "Arachnida", "Arachnida", "Insec…
$ order       <chr> "Araneae", "Araneae", "Araneae", "Araneae", "Coleoptera", …
$ suborder    <chr> NA, NA, NA, NA, "Adephaga", "Phytophaga", "Phytophaga", "P…
$ family      <chr> NA, NA, NA, NA, "Dytiscidae", "Curculionidae", "Curculioni…
$ subfamily   <lgl> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…
$ juvenile    <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ terrestrial <dbl> 1, 1, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ juv.aquatic <dbl> 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ unusable    <dbl> 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0…
$ size        <dbl> 2, 2, 2, 2, 5, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2…
$ Laufnummer  <dbl> 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137, 137…

Metadatada:

data_dict <- data.frame(
  Column_name = c(
    "site", "location", "date", "class", "order", "suborder", "family",
    "subfamily", "juvenile", "terrestrial", "juv aquatic", "unusable",
    "size", "remarks"
  ),
  Explanation = c(
    "Study system in which the individual was sampled",
    "Site at which individual was sampled (i.e. pool or control)",
    "Collection period during which the individual was sampled (i.e. June or July)",
    "Taxonomic class the sampled individual belongs to",
    "Taxonomic order the sampled individual belongs to",
    "Taxonomic suborder the sampled individual belongs to (where available)",
    "Taxonomic family the sampled individual belongs to (where available)",
    "Taxonomic subfamily the sampled individual belongs to (where available)",
    "Binary value indicating if the sampled individual was a juvenile. 1 = juvenile, 0 = adult",
    "Binary value indicating if the sampled individual was winged. 1 = non-winged, 0 = winged",
    "Binary value indicating if the sampled individual belongs to a taxa with purely aquatic juveniles. 1 = aquatic, 0 = not aquatic",
    "Binary value indicating if the sampled individual came from water (amphipoda, gastropoda)",
    "Length of the sampled individual in mm (rounded to full numbers). Measured from head to end of abdomen, excluding appendages (wings, limbs, antennae, cerci, etc.)",
    "Additional comments or information about a given individual"
  )
)

kable(data_dict, align = c("l","l"), caption = "Metadata for data_arthropods_flying.xlsx")

Metadata for data_arthropods_flying.xlsx

Column_name	Explanation
site	Study system in which the individual was sampled
location	Site at which individual was sampled (i.e. pool or control)
date	Collection period during which the individual was sampled (i.e. June or July)
class	Taxonomic class the sampled individual belongs to
order	Taxonomic order the sampled individual belongs to
suborder	Taxonomic suborder the sampled individual belongs to (where available)
family	Taxonomic family the sampled individual belongs to (where available)
subfamily	Taxonomic subfamily the sampled individual belongs to (where available)
juvenile	Binary value indicating if the sampled individual was a juvenile. 1 = juvenile, 0 = adult
terrestrial	Binary value indicating if the sampled individual was winged. 1 = non-winged, 0 = winged
juv aquatic	Binary value indicating if the sampled individual belongs to a taxa with purely aquatic juveniles. 1 = aquatic, 0 = not aquatic
unusable	Binary value indicating if the sampled individual came from water (amphipoda, gastropoda)
size	Length of the sampled individual in mm (rounded to full numbers). Measured from head to end of abdomen, excluding appendages (wings, limbs, antennae, cerci, etc.)
remarks	Additional comments or information about a given individual

Note

Question:

How many taxa which ones are there?

# Get unique families (excluding NA)
families <- unique(na.omit(d$family))

# Number of unique families
num_families <- length(families)

# Print results
cat("Number of unique families:", num_families, "\n\n")

Number of unique families: 29 

cat("Families:\n")

Families:

print(sort(families))

 [1] "Aphidoidea"    "Cantharidae"   "Carabidae"     "Chrysomelidae"
 [5] "Coccinellidae" "Cucujidae"     "Curculionidae" "Dytiscidae"   
 [9] "Elmidae"       "Erebidae"      "Forficulidae"  "Formicidae"   
[13] "Gerridae"      "Gyrinidae"     "Haliplidae"    "Hydrophilidae"
[17] "Latridiidae"   "Monotomidae"   "Mordellidae"   "Nitidulidae"  
[21] "Notonectidae"  "Panorpidae"    "Phalacridae"   "Psylloidea"   
[25] "Scirtidae"     "Staphylinidae" "Syrphidae"     "Tabanidae"    
[29] "Vespidae"     

Description of the families we have found:

# Families Found Near Streams in Switzerland

families_table <- data.frame(
  Family = c(
    "Aphidoidea", "Cantharidae", "Carabidae", "Chrysomelidae",
    "Coccinellidae", "Cucujidae", "Curculionidae", "Dytiscidae",
    "Elmidae", "Erebidae", "Forficulidae", "Formicidae",
    "Gerridae", "Gyrinidae", "Haliplidae", "Hydrophilidae",
    "Latridiidae", "Monotomidae", "Mordellidae", "Nitidulidae",
    "Notonectidae", "Panorpidae", "Phalacridae", "Psylloidea",
    "Scirtidae", "Staphylinidae", "Syrphidae", "Tabanidae",
    "Vespidae"
  ),
  Description = c(
    "Aphids; plant sap-feeders, often found on riparian vegetation.",
    "Soldier beetles; predatory or nectar-feeding, common in meadows near water.",
    "Ground beetles; many species are predators along stream banks.",
    "Leaf beetles; herbivores on riparian plants.",
    "Lady beetles; mostly aphid predators on vegetation.",
    "Flat bark beetles; live under bark, sometimes in moist riparian wood.",
    "Weevils; herbivores feeding on riparian plants and shrubs.",
    "Predaceous diving beetles; aquatic predators in streams and ponds.",
    "Riffle beetles; aquatic, live attached to stones in running water.",
    "Tiger moths and relatives; larvae feed on diverse plants near water.",
    "Earwigs; omnivores hiding under stones and wood along streams.",
    "Ants; common in soils and vegetation along riparian zones.",
    "Water striders; aquatic predators skating on water surfaces.",
    "Whirligig beetles; fast swimmers on water surfaces in streams.",
    "Crawling water beetles; small herbivorous beetles in shallow water.",
    "Water scavenger beetles; aquatic or semi-aquatic scavengers.",
    "Minute brown scavenger beetles; found in decaying plant matter.",
    "Root-eating beetles; often associated with decaying wood.",
    "Tumbling flower beetles; found on flowers near riparian habitats.",
    "Sap beetles; feed on decaying fruit, fungi, and plant material.",
    "Backswimmers; aquatic predators that swim upside down.",
    "Scorpionflies; scavengers, often in damp shaded stream habitats.",
    "Shining flower beetles; small pollen feeders.",
    "Psyllids; plant sap-feeders, often on riparian trees and shrubs.",
    "Marsh beetles; aquatic or semi-aquatic beetles in wetlands.",
    "Rove beetles; very diverse predators and scavengers in moist habitats.",
    "Hoverflies; larvae are aphid predators, adults visit flowers.",
    "Horse flies; adults feed on blood or nectar, larvae in wet soils.",
    "Wasps; diverse group of predators and parasitoids near water."
  )
)

kable(families_table, caption = "Ecological roles of arthropod families sampled close to streams in Switzerland")

Ecological roles of arthropod families sampled close to streams in Switzerland

Family	Description
Aphidoidea	Aphids; plant sap-feeders, often found on riparian vegetation.
Cantharidae	Soldier beetles; predatory or nectar-feeding, common in meadows near water.
Carabidae	Ground beetles; many species are predators along stream banks.
Chrysomelidae	Leaf beetles; herbivores on riparian plants.
Coccinellidae	Lady beetles; mostly aphid predators on vegetation.
Cucujidae	Flat bark beetles; live under bark, sometimes in moist riparian wood.
Curculionidae	Weevils; herbivores feeding on riparian plants and shrubs.
Dytiscidae	Predaceous diving beetles; aquatic predators in streams and ponds.
Elmidae	Riffle beetles; aquatic, live attached to stones in running water.
Erebidae	Tiger moths and relatives; larvae feed on diverse plants near water.
Forficulidae	Earwigs; omnivores hiding under stones and wood along streams.
Formicidae	Ants; common in soils and vegetation along riparian zones.
Gerridae	Water striders; aquatic predators skating on water surfaces.
Gyrinidae	Whirligig beetles; fast swimmers on water surfaces in streams.
Haliplidae	Crawling water beetles; small herbivorous beetles in shallow water.
Hydrophilidae	Water scavenger beetles; aquatic or semi-aquatic scavengers.
Latridiidae	Minute brown scavenger beetles; found in decaying plant matter.
Monotomidae	Root-eating beetles; often associated with decaying wood.
Mordellidae	Tumbling flower beetles; found on flowers near riparian habitats.
Nitidulidae	Sap beetles; feed on decaying fruit, fungi, and plant material.
Notonectidae	Backswimmers; aquatic predators that swim upside down.
Panorpidae	Scorpionflies; scavengers, often in damp shaded stream habitats.
Phalacridae	Shining flower beetles; small pollen feeders.
Psylloidea	Psyllids; plant sap-feeders, often on riparian trees and shrubs.
Scirtidae	Marsh beetles; aquatic or semi-aquatic beetles in wetlands.
Staphylinidae	Rove beetles; very diverse predators and scavengers in moist habitats.
Syrphidae	Hoverflies; larvae are aphid predators, adults visit flowers.
Tabanidae	Horse flies; adults feed on blood or nectar, larvae in wet soils.
Vespidae	Wasps; diverse group of predators and parasitoids near water.

Plot data

# Alternative: side-by-side histogram (use 'dodge')
ggplot(d, aes(x = size, fill = location)) +
  geom_histogram(binwidth = 1, color = "black", alpha = 0.7, position = "dodge") +
  labs(
    title = "Histogram of individual sizes by sampled location",
    x = "Size (mm)",
    y = "Frequency",
    fill = "Location"
  ) +
  theme_bw(base_size = 14)

ggplot(d, aes(y = location, x = size, fill = location)) +
  stat_halfeye(position = "dodge",
    adjust = 1,       # smoothness of density
    width = 0.6,        # width of half-eye
    justification = -0.1,
    point_interval = mean_qi,  # show mean & 95% interval
    alpha = 0.7
  ) +
  labs(
    title = "Size Distributions by Location",
    y = "Location",
    x = "Size (mm)"
  ) +
  theme_bw(base_size = 14)

References